I've read several conflicting stories about this. One story I've read says that "Joe" actually stands for Jolt Of Energy, and was a slang term that the army used. Another story claims that the reference actually came from the Navy, where a high ranking official named Josephus banned wine and wouldn't allow sailors to drink anything stronger than coffee, earning it the nickname "cup of Joe". Still another story claims that it's called a "cup of Joe" because "Joe" is a common name and coffee is a common man's drink. I have no clue which of these are true, or if they are all false!

Joe or Cup of Joe – the name goes back to the mid 1840’s when the Secretary of the Navy, Josephus Daniels prohibited alcohol consumption on ships. He has ordered that mariners should be served only coffee instead. Thus, a cup of coffee began to be called “a cup of Joe”. However, it is still an open question because there is a version that the famous phrase has been put in practice much earlier than this event.